Effects of metal and metalloid pollutants on the microbiota composition of feces obtained from twelve commercial pig farms across China

Temporal dynamics of microbial composition and antibiotic resistome in fermentation bed culture pig farms across various ages

The discharge from pig farms presents significant challenges to the environment and human health, specifically regarding the dissemination of antimicrobial resistance (AMR). Fermentation bed culture has emerged as an increasingly popular and environmentally friendly pig farming model in China, as it minimizes the release of harmful substances into the environment. However, there remains a limited understanding of the occurrence and dynamics of microbiome and antibiotic resistome in fermentation bed culture. Herein, we collected fermentation bed materials (FBM) from four fermentation bed culture pig farms with varying service ages and investigated their bacterial communities, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metal resistance genes (MRGs) and potential antibiotic-resistant bacterial hosts through metagenomics. Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota were identified as the dominant phyla present in the FBM. In total, we detected 258 unique ARGs in the FBM samples, with 79 core ARGs shared by all FBM samples, accounting for 95 % of the total ARG abundance. Our results revealed significant variations in microbial communities and ARG profiles across varying service ages of FBM. Compared to long-term FBW, short-term FBM exhibited higher numbers and abundances of ARGs, MRGs and MGEs, along with higher levels of potential bacterial pathogens and high-risk ARGs. Further analysis of metagenome-assembled genome (MAG) indicated that the putative hosts of ARGs primarily belonged to Pseudomonadota, Actinomycetota and Bacillota. Alarmingly, among the 80 recovered ARG-carrying MAGs, 23 MAGs encoded multi-resistance, including clinically significant species that require urgent attention. Overall, this study provided valuable insights into the temporal patterns of antibiotic resistome and bacterial communities within FBM, enhancing our understanding of FBM in pig farming. The findings could potentially contribute to the development of effective strategies for evaluating and regulating fermentation bed culture practices in pig farming.

Insights into antibiotic and heavy metal resistance interactions in Escherichia coli isolated from livestock manure and fertilized soil

Heavy metal and antibiotic-resistant bacteria from livestock feces are ecological and public health problems. However, the distribution and relationships of antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRGs), and virulence factors (VFs) and their transmission mechanisms remain unclear. Therefore, we investigated the resistance of Escherichia coli, the prevalence of its ARGs, HMRGs, and VFs, and their transmission mechanisms in livestock fresh feces (FF), composted feces (CF), and fertilized soil (FS). In total, 99.54% (n = 221) and 91.44% (n = 203) of E. coli were resistant to at least one antibiotic and one heavy metal, respectively. Additionally, 72.52% (n = 161) were multi-drug resistant (MDR), of which Cu-resistant E. coli accounted for 72.67% (117/161). More than 99.34% (88/89) of E. coli carried multidrug ARGs, VFs, and the Cu resistance genes cueO and cusABCRFS. The Cu resistance genes cueO and cusABCRFS were mainly located on chromosomes, and cueO and cusF were positively associated with HMRGs, ARGs, and VFs. The Cu resistance genes pcoABCDRS were located on the plasmid pLKYL-P02 flanked by ARGs in PF18C from FF group and on chromosomes flanked by HMRGs in SAXZ1-1 from FS group. These results improved our understanding of bacterial multidrug and heavy metal resistance in the environment.

Recovery of Copper and Zinc from Livestock Bio-Sludge with An Environmentally Friendly Organic Acid Extraction

Pig farmers in Taiwan tend to overdose copper (Cu) and zinc (Zn) in animal feeds to ensure pig health. The application of Cu- or Zn-rich livestock compost to fields can result in high Cu/Zn residues in surface soil and violate limitations for zinc and copper in land applications. This study aims to extract Cu and Zn from sludge using organic acid or H2O2/organic acids. The livestock bio-sludge was dried and treated with different concentrations of acetic acid (1N, 2N, and 4N). The acid-extracted sludge was then treated with or without adding H2O2 during different periods (4, 24, and 48 h) to investigate the efficiency of acid extraction of Cu and Zn. The supernatant of the acid-extracted product was separated from the residues through centrifugation. Experimental results showed that the treatment set of dried bio-sludge with 2% H2O2 significantly promoted the removal efficiency of Cu and Zn from the bio-sludge (p < 0.01). The best removal efficiency of Cu and Zn from the bio-sludge was 40% and 70%, respectively, using 4N acetic acid in the 48 h group. The study shows a green method for extracting Cu and Zn from livestock sludge, enhancing the sustainability of intensive livestock farming.

Bioactive compounds, antibiotics and heavy metals: effects on the intestinal structure and microbiome of monogastric animals – a non-systematic review

The intestinal structure and gut microbiota are essential for the animals‘ health. Chemical components taken with food provide the right environment for a specific microbiome which, together with its metabolites and the products of digestion, create an environment, which in turn is affects the population size of specific bacteria. Disturbances in the composition of the gut microbiota can be a reason for the malformation of guts, which has a decisive impact on the animal‘ health. This review aimed to analyse scientific literature, published over the past 20 years, concerning the effect of nutritional factors on gut health, determined by the intestinal structure and microbiota of monogastric animals. Several topics have been investigated: bioactive compounds (probiotics, prebiotics, organic acids, and herbal active substances), antibiotics and heavy metals (essentaial minerals and toxic heavy metals).

Mitochondrial miR-1285 regulates copper-induced mitochondrial dysfunction and mitophagy by impairing IDH2 in pig jejunal epithelial cells

Copper (Cu), a hazardous heavy metal, can lead to toxic effects on host physiology. Recently, specific mitochondria-localized miRNAs (mitomiRs) were shown to modulate mitochondrial function, but the underlying mechanisms remain undefined. Here, we identified mitomiR-1285 as an important molecule regulating mitochondrial dysfunction and mitophagy in jejunal epithelial cells under Cu exposure. Mitochondrial dysfunction and mitophagy were the important mechanisms of Cu-induced pathological damage in jejunal epithelial cells, which were accompanied by significant increase of mitomiR-1285 in vivo and in vitro. Knockdown of mitomiR-1285 significantly attenuated Cu-induced mitochondrial respiratory dysfunction, ATP deficiency, mitochondrial membrane potential reduction, mitochondrial reactive oxygen species accumulation, and mitophagy. Subsequently, bioinformatics analysis and luciferase reporter assay demonstrated that IDH2 was a direct target of mitomiR-1285. RNA interference of IDH2 dramatically reversed the effect that mitomiR-1285 knockdown relieved mitochondrial dysfunction and mitophagy induced by Cu, and the opposite effect was shown by overexpression of IDH2. Therefore, our results suggested that mitomiR-1285 aggravated Cu-induced mitochondrial dysfunction and mitophagy via suppressing IDH2 expression. These findings identified the important mechanistic connection between mitomiRs and mitochondrial metabolism under Cu exposure, providing a new insight into Cu toxicology.

Natural treatment system for wastewater (NTSW) in a livestock farm, with five years of pilot plant management and monitoring

This paper reports results of a 5-year trial study of a natural treatment system for wastewater (NTSW) on a livestock pig farm on Gran Canaria (Canary Islands, Spain). The pilot plant consist of a rotary screen, a first-generation multi-chamber digester, and two horizontal subsurface flow treatment wetlands (HSFCW) with a pond installed between them. Results show that the removal efficiency of total chemical oxygen demand (CODt), total suspended solids (TSS), volatile solids (VS) and total dissolved solids (TDS) of the treatment were 91.77%, 95.99%, 82.62%, and 55.78%, respectively. Other removal values include 93.79% for total nitrogen (TN) and 93.05% for phosphorus (P₂O₅). The results demonstrate the suitability of NTSW solutions applied to livestock waste in pig farms and their potential application to other farms of similar size.

Trace metals and animal health: Interplay of the gut microbiota with iron, manganese, zinc, and copper

Metals such as iron, manganese, copper, and zinc are recognized as essential trace elements. These trace metals play critical roles in development, growth, and metabolism, participating in various metabolic processes by acting as cofactors of enzymes or providing structural support to proteins. Deficiency or toxicity of these metals can impact human and animal health, giving rise to a number of metabolic and neurological disorders. Proper breakdown, absorption, and elimination of these trace metals is a tightly regulated process that requires crosstalk between the host and these micronutrients. The gut is a complex system that serves as the interface between these components, but other factors that contribute to this delicate interaction are not well understood. The gut is home to trillions of microorganisms and microbial genes (the gut microbiome) that can regulate the metabolism and transport of micronutrients and contribute to the bioavailability of trace metals through their assimilation from food sources or by competing with the host. Furthermore, deficiency or toxicity of these metals can modulate the gut microenvironment, including microbiota, nutrient availability, stress, and immunity. Thus, understanding the role of the gut microbiota in the metabolism of manganese, iron, copper, and zinc, as well as in heavy metal deficiencies and toxicities, and vice versa, may provide insight into developing improved or alternative therapeutic strategies to address emerging health concerns. This review describes the current understanding of how the gut microbiome and trace metals interact and affect host health, particularly in pigs.

Behaviors of cadmium in rhizosphere soils and its interaction with microbiome communities in phytoremediation

Phytoremediation of cadmium (Cd) contaminated soils by accumulators or hyperaccumulators has received considerable attention. However, there is still limited information about its migration, dynamic characteristics, and interaction with microbial communities in rhizosphere. In this study, the behaviors of Cd in rhizosphere soils in phytoremediation were carefully studied and illustrated. We find that the migration rate of Cd in rhizosphere is higher than the absorption rate of Cd by roots of plants, and Cd in near-rhizosphere moves sluggishly, and near-rhizosphere soils forms a mass pool of Cd for absorption by plants. Additionally, in tall fescue and Indian mustard treatments, shoot biomasses, total extracted Cd and migration rate of Cd in near-rhizosphere soils were comparable. It suggests that shoot biomasses of plants significantly affect their extraction of heavy metals from rhizosphere soils. Biomasses of bacteria significantly increased after phytoremediation, and structures of microbiome communities of soils after phytoremediation reassembled significantly. Furthermore, Indian mustard, even with relative lower root biomasses, could better reassembled the microbiome communities in rhizosphere than tall fescue which possesses a higher developed root system. In the end, analyses of functional microorganisms in rhizosphere soils provide new insights into biological and physiochemical roles of these populations in phytoremediation.

Influence of different dietary oil consumption on nutrient malabsorption: An animal trial using Sprague Dawley rats

In the present study, the influences of five typical dietary oils (i.e., palm oil, PO; leaf lard oil, LO; rapeseed oil, RO; sunflower oil, SO; and linseed oil, LN) consumption on the nutrients malabsorption were studied using adult male Sprague Dawley rats. Results suggested that the C16:0 (24.534 ± 2.26% to 54.269 ± 1.28%) and C18:0 (18.433 ± 4.421% to 36.455 ± 3.316%) were the dominant fatty acids in fecal samples in different groups. After 6-week intervention by different dietary oils, the fecal moisture and water soluble protein content in PO group, the reducing sugar content in PO, LO, and RO groups were significantly increased compared with those in the control group (p < .05). Moreover, the Na, K, and Fe contents in LO group were all the highest among the all groups. These effects were probably due to the different fatty acids composition as illustrated in the correlation analysis results. The different effects were probably due to their distinct fatty acids composition as illustrated in the correlation analysis results. Results further indicated that the different dietary oils treatment, especially for the PO (SFAs, 43.17 ± 0.98%) and LO (SFAs, 36.44 ± 0.65%), increased the upstream inflammatory cytokine expression level in the Toll-like receptor signal pathway (i.e., TLR4 and MyD88), enhancing the gut permeability. This resulted in significant increase of serum lipopolysaccharide (LPS) levels (p < .05), which was closely connected with different metabolic diseases. The present study may provide basic understandings about different dietary oil enteral nutrition and their effects on gut health. PRACTICAL APPLICATIONS: The PO, LO, RO, SO, and LN are the five of the most typical dietary lipids in Asia countries, especially in China. They are the natural edible oils which are rich in C16:0, C18:0, C18:1, C18:2ω6, and C18:3ω3, respectively. The present study indicated that the different dietary lipid consumption may result in different dietary nutrients malabsorption, which are related with the dietary lipid fatty acid composition.

Zinc Supplementation Forms Influenced Zinc Absorption and Accumulation in Piglets

The study aimed at determining the effect of different zinc (Zn) supplementation forms on Zn accumulation, activities of Zn-containing enzymes, gene expression of metallothionein (MT), and Zn transporters in piglets. Eighteen piglets were randomly divided into three groups: (a) a basal diet supplemented with 150 mg/kg Zn from Zn methionine (Zn-Met) in the feed (Zn-Met group), (b) a basal diet supplemented with 150 mg/kg Zn from Zn sulfate (ZnSO₄) in the feed (ZnSO₄, _feed group), and (c) a basal diet supplemented with the same dose of Zn as in ZnSO4,_feed group but in water (ZnSO₄, _water group). The results showed that Zn-Met added in feed and ZnSO₄ dissolved in drinking water significantly improved (p < 0.05) the Zn concentration in liver and jejunum and the apparent digestibility of Zn in comparison with the ZnSO₄ added in feed. In addition, dietary Zn supplementation as Zn-Met significantly increased (p < 0.05) the activity of alkaline phosphatase (AKP) in the jejunum of piglets in comparison with the ZnSO₄, _feed group. Furthermore, the Zn-Met and ZnSO₄, _water groups showed an improved total superoxide dismutase activity (T-SOD) in the ileum as compared to the ZnSO₄, _feed group. Meanwhile, the qPCR and western blot results showed that Zn-Met and ZnSO₄ dissolved in drinking water increased the expression of MT in the jejunum in comparison with the ZnSO₄ added in the piglets' feed. However, different Zn supplementation forms had no effect on the mRNA expressions of Zip4 and ZnT1 transporters. In conclusion, Zn-Met added in feed and ZnSO₄ dissolved in drinking water had higher bioavailability in piglets.

Microbial diversity of representative traditional fermented sausages in different regions of China

AIMS

The purpose of this experiment was to study the bacterial diversity of traditional fermented sausages from four typical regions of China (Chengdu, Shenzhen, Changsha and Harbin) and to further evaluate their microbiological safety.

METHODS AND RESULTS

The diversity of the microbiota of the sausages was studied using the Illumina HiSeq platform. The results showed that compared with the highest diversity of fermented bacteria in Guangdong, the bacterial diversity of fermented sausage was the lowest in Sichuan. The percentage of dominant phylum (Firmicutes, Cyanophyta, Proteobacter) were 78·39, 13·13 and 7·14% in SC, 35·47, 30·36 and 28·04% in GD, 54·81, 28·91 and 14·00% in HN, 20·20, 58·16 and 17·31% in HB respectively. The main genus distribution of fermented sausages in different regions is varied, but lactic acid bacteria and cyanobacteria are generally the main ones. Traditional fermented sausages using natural fermentation methods have poor microbiological safety, and pathogenic and spoilage micro-organisms such as Acinetobacter, Brochothrix and Pseudomonas have been detected in all four regions.

CONCLUSIONS

The results in this paper provide a microbiota profile of four typical fermented sausages in China. There is a big difference in the microbiota of sausages in different regions, and the good flavour of traditional Chinese fermented sausage is related closely with the abundant microbial resources, however, the natural fermentation method also expose to the product security threats, including spoilage, pathogenic micro-organisms and biogenic amines, etc. SIGNIFICANCE AND IMPACT OF THE STUDY: The results would offer guidance for industrial fermented sausage production with certain flavour and also improve the microbial resource utilization, and contribute to the control of harmful micro-organisms in traditional fermented sausage.

Comparison of Rumen Microbiota and Serum Biochemical Indices in White Cashmere Goats Fed Ensiled or Sun-Dried Mulberry Leaves

Mulberry leaves, which have high nutritional value, have not been fully utilized. Few research systems have indicated whether mulberry leaves can replace traditional feed ingredients in goats. In this study, we investigated the effects of feeding white cashmere goats ensiled (Group E) or sun-dried mulberry leaves (Group S) on changes in ruminal microbial communities, rumen fermentation parameters and serum biochemical indices. The control group (Group C) received a typical total mixed ration (TMR). 16S rRNA gene sequencing revealed 209 genera belonging to 19 bacterial phyla dominated by Firmicutes and Bacteroidetes. Only the relative abundances of Erysipelotrichaceae_UCG-009 were significantly different among the three groups (p < 0.05). Physiological and biochemical findings revealed that only the serum leptin concentrations were significantly decreased when mulberry leaves were added to the diets (p < 0.05). Correlation analysis revealed that Ruminococcus_2 were significantly positively correlated with the butyrate concentration. These findings suggested that supplementation with mulberry leaves only induced minor changes in the abovementioned indicators, implying that the rumen fermentation status was still stable after adding mulberry leaves to the diets.